Variant report

Variant	rs2275425
Chromosome Location	chr1:46489051-46489052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46486434..46490068-chr1:46491695..46494942,4	K562	blood:
2	chr1:46152249..46154389-chr1:46489050..46491985,2	K562	blood:
3	chr1:46486510..46488331-chr1:46488785..46491782,2	MCF-7	breast:
4	chr1:46488776..46491318-chr1:46492009..46494441,2	K562	blood:

Variant related genes	Relation type
ENSG00000086015	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12119176	1.00[EUR][1000 genomes]
rs17102066	1.00[AMR][1000 genomes]
rs2282333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28363193	1.00[AMR][1000 genomes]
rs41292274	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41378047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41401147	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4297232	1.00[AMR][1000 genomes]
rs4420029	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs57121950	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57402001	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57959845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57991520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58888694	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59669845	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59768249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59919818	1.00[AMR][1000 genomes]
rs59974520	1.00[AMR][1000 genomes]
rs60789947	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60933200	1.00[AMR][1000 genomes]
rs61169182	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61178863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7542465	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv546158	chr1:46216575-46495434	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv870911	chr1:46216575-46498375	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv431268	chr1:46223080-46495480	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1007759	chr1:46248667-46493959	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv534945	chr1:46248667-46493959	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv916232	chr1:46248686-46493918	Genic enhancers Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv1009527	chr1:46286329-46520127	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
14	nsv546161	chr1:46311275-46498375	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
17	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
18	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
19	nsv829737	chr1:46352900-46506424	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
21	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
22	nsv522438	chr1:46462881-46500993	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
23	esv1795204	chr1:46466373-46504466	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
24	esv1829371	chr1:46466373-46504466	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
25	nsv1007750	chr1:46471293-46552564	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
26	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
27	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46470600-46489800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:46473000-46500400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:46473600-46502600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr1:46474400-46502600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:46474600-46490400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:46474600-46496600	Weak transcription	Fetal Thymus	thymus
7	chr1:46475600-46525000	Weak transcription	Fetal Kidney	kidney
8	chr1:46476200-46502600	Weak transcription	Stomach Mucosa	stomach
9	chr1:46476400-46495200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:46476600-46515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:46477400-46489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:46477400-46493800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:46477400-46496000	Weak transcription	Small Intestine	intestine
14	chr1:46483600-46489200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:46484600-46492000	Strong transcription	Brain Germinal Matrix	brain
16	chr1:46484800-46502000	Strong transcription	Fetal Intestine Small	intestine
17	chr1:46485000-46502000	Strong transcription	Fetal Stomach	stomach
18	chr1:46485400-46491800	Strong transcription	Fetal Intestine Large	intestine
19	chr1:46485800-46503000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:46486200-46489600	Strong transcription	Right Ventricle	heart
21	chr1:46486400-46491600	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr1:46486600-46490000	Strong transcription	Aorta	Aorta
23	chr1:46486600-46491000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:46486600-46491800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:46486600-46492200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:46486800-46490200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:46486800-46490200	Strong transcription	HepG2	liver
28	chr1:46486800-46491800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:46486800-46502400	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:46487000-46489200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:46487000-46489600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:46487000-46490200	Strong transcription	Brain Angular Gyrus	brain
33	chr1:46487000-46490200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:46487000-46490200	Strong transcription	Fetal Lung	lung
35	chr1:46487000-46490400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:46487000-46490400	Strong transcription	K562	blood
37	chr1:46487000-46491400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:46487000-46491600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:46487000-46491600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:46487000-46491600	Strong transcription	Placenta	Placenta
41	chr1:46487000-46496600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:46487000-46502000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr1:46487200-46489200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:46487200-46489600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:46487200-46489800	Weak transcription	Fetal Heart	heart
46	chr1:46487200-46490200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:46487200-46490200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr1:46487200-46490800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:46487200-46491400	Strong transcription	Dnd41	blood
50	chr1:46487200-46491600	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links